Biomedical subjects

Robin C Ball

Publications and source records attributed to Robin C Ball.

8 recordsLinked to original sources

PubMed2005

Off-lattice noise reduced diffusion-limited aggregation in three dimensions.

Using off-lattice noise reduction, it is possible to estimate the asymptotic properties of diffusion-limited aggregation clusters grown in three dimensions with greater accuracy than would otherwise be possible. The fractal dimension of these aggregates is found to be 2.50+/-0.01 , in agreement with earlier studies, and the asymptotic value of the relative penetration depth is xi/ R(dep) =0.122+/-0.002 . The multipole powers of the growth measure also exhibit universal asymptotes. The fixed point noise reduction is estimated to be epsilon(f) approximately 0.0035 , meaning that large clusters can be identified with a low noise regime. The slowest correction to scaling exponents are measured for a number of properties of the clusters, and the exponent for the relative penetration depth and quadrupole moment are found to be significantly different from each other. The relative penetration depth exhibits the slowest correction to scaling of all quantities, which is consistent with a theoretical result derived in two dimensions. We also note fast corrections to scaling, whose limited relevance is consistent with the requirement that clusters grow far enough in radius to support sufficient scales of ramification.

Journal Article↗

PubMed2004

Growth by random walker sampling and scaling of the dielectric breakdown model.

Random walkers absorbing on a boundary sample the harmonic measure linearly and independently: we discuss how the recurrence times between impacts enable nonlinear moments of the measure to be estimated. From this we derive a technique to simulate dielectric breakdown model growth, which is governed nonlinearly by the harmonic measure. For diffusion-limited aggregation, recurrence times are shown to be accurate and effective in probing the multifractal growth measure in its active region. For the dielectric breakdown model our technique grows large clusters efficiently and we are led to significantly revise earlier exponent estimates. Previous results by two conformal mapping techniques were less converged than expected, and in particular a recent theoretical suggestion of superuniversality is firmly refuted.

Journal Article↗

PubMed2003

Characterization of the probabilistic traveling salesman problem.

We show that stochastic annealing can be successfully applied to gain new results on the probabilistic traveling salesman problem. The probabilistic "traveling salesman" must decide on an a priori order in which to visit n cities (randomly distributed over a unit square) before learning that some cities can be omitted. We find the optimized average length of the pruned tour follows E(L(pruned))=sqrt[np](0.872-0.105p)f(np), where p is the probability of a city needing to be visited, and f(np)-->1 as np--> infinity. The average length of the a priori tour (before omitting any cities) is found to follow E(L(a priori))=sqrt[n/p]beta(p), where beta(p)=1/[1.25-0.82 ln(p)] is measured for 0.05< or =p< or =0.6. Scaling arguments and indirect measurements suggest that beta(p) tends towards a constant for p<0.03. Our stochastic annealing algorithm is based on limited sampling of the pruned tour lengths, exploiting the sampling error to provide the analog of thermal fluctuations in simulated (thermal) annealing. The method has general application to the optimization of functions whose cost to evaluate rises with the precision required.

Journal Article↗

PubMed2003

Diffusion-limited aggregation in channel geometry.

We performed extensive numerical simulation of diffusion-limited aggregation in two-dimensional channel geometry. Contrary to earlier claims, the measured fractal dimension D=1.712+/-0.002 and its leading correction to scaling are the same as in the radial case. The average cluster, defined as the average conformal map, is similar but not identical to Saffman-Taylor fingers.

Journal Article↗

PubMed2003

Stochastic annealing.

We show how to simulate a system in thermal equilibrium when the energy cannot be evaluated exactly: the error distribution needs to be symmetric, but it does not need to be known. We also solve the Ceperley-Dewing version of this problem, where the error distribution is taken to be fully known. These underlying ideas give an effective optimization strategy for problems where the evaluation of each design can be sampled only statistically, including an application to protein folding.

Models, Statistical↗

PubMed2002

Protein design depends on the size of the amino acid alphabet.

We consider the design of proteins to be simultaneously thermodynamically stable in multiple independent and correlated conformations. We first show that a protein can be trained to fold to multiple independent conformations and calculate its capacity. The number of configurations that it can remember is proportional to the logarithm of the number of amino acid species A, independent of chain length. Next we investigate the recognition of correlated conformations, which we apply to funnel design around a single configuration. The maximum basin of attraction, as parametrized in our model, also depends on the number of amino acid species as ln A. We argue that the extent to which the protein energy landscape can be manipulated is fixed, effecting a trade off between well breadth, well depth, and well number. This emerging picture motivates a clearer understanding of the scope and limits of protein and heteropolymer function.

Amino Acids↗

PubMed2002

Off-lattice noise reduction and the ultimate scaling of diffusion-limited aggregation in two dimensions.

Off-lattice diffusion-limited aggregation (DLA) clusters grown with different levels of noise reduction are found to be consistent with a simple fractal fixed point. Cluster shapes and their ensemble variation exhibit a dominant slowest correction to scaling, and this also accounts for the apparent "multiscaling" in the DLA mass distribution. We interpret the correction to scaling in terms of renormalized noise. The limiting value of this variable is strikingly small and is dominated by fluctuations in cluster shape. Earlier claims of anomalous scaling in DLA were misled by the slow approach to this small fixed point value.

Journal Article↗

PubMed2002

Stress field in granular systems: loop forces and potential formulation.

The transmission of stress through a marginally stable granular pile in two dimensions is exactly formulated in terms of a vector field of loop forces, and thence in terms of a single scalar potential. This leads to a local constitutive equation coupling the stress tensor to fluctuations in the local geometry. For a disordered pile of rough grains this means the stress tensor components are coupled in a frustrated manner. In piles of rough grains with long range staggered order, frustration is avoided and a simple linear theory follows. We show that piles of smooth grains can be mapped onto a pile of unfrustrated rough grains, indicating that the problems of rough and smooth grains may be fundamentally distinct.

Journal Article↗